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Archive for the ‘PubMed’ Category

NLM Releases Extensible Markup Language (XML) for IndexCat™ Data

The National Library of Medicine has announced that Extensible Markup Language (XML) data from the IndexCat™ database is now available for free download. Released with a Document Type Definition (DTD) that allows researchers to validate the data, this new XML release includes the digitized content of more than 3.7 million bibliographic items from the printed, 61-volume Index-Catalogue of the Library of the Surgeon-General’s Office, originally published from 1880 to 1961. The XML describes items spanning five centuries, including millions of journal and newspaper articles, obituaries, and letters; hundreds of thousands of monographs and dissertations; and thousands of portraits. Together, these items cover a wide range of subjects such as the basic sciences, scientific research, civilian and military medicine, public health, and hospital administration.

The NLM release of the Index-Catalogue in XML format opens this key resource in the history of medicine and science to new uses and users. It is one of the monuments of the Library’s longstanding, systematic indexing of the medical literature, an effort which William Henry Welch (1850-1934), the great pathologist and bibliophile, considered to be “America’s greatest contribution to medical knowledge.” This indexing, begun by John Shaw Billings in the nineteenth century at the Library of the Surgeon-General’s Office, United States Army (known today as the NLM), eventually created two distinct products: the Index-Catalogue of the Library of the Surgeon-General’s Office, United States Army, and the Index Medicus, forerunner of MEDLINE®, and now the largest component of PubMed

Released alongside the IndexCatalogue XML are an integrated XML file and associated DTD for two collections developed from the electronic database of A Catalogue of Incipits of Mediaeval Scientific Writings in Latin (rev.), by Lynn Thorndike and Pearl Kibre (eTK), and the updated and expanded version of Scientific and Medical Writings in Old and Middle English: An Electronic Reference (eVK2), edited by Linda Ehrsam Voigts and Patricia Deery Kurtz. Also available via the online IndexCat, these resources encompass over 42,000 records of incipits, or the beginning words of a medieval manuscript or early printed book, covering various medical and scientific writings on topics as diverse as astronomy, astrology, geometry, agriculture, household skills, book production, occult science, natural science, and mathematics, as these disciplines and others were largely intermingled in the medieval period of European history. The NLM release of these resources in XML format joins many other freely downloadable resources, including the XML for MEDLINE®/PubMed® data, which includes over 22 million references to biomedical and life sciences journal articles back to 1946, and, for some journals, much earlier.

The release also coincides with the NLM’s participation in “Shared Horizons: Data, Biomedicine, and the Digital Humanities,” an interdisciplinary symposium exploring the intersection of digital humanities and biomedicine, being held April 10-12, 2013, in partnership with the National Endowment for the Humanities’ Office of Digital Humanities, Maryland Institute for Technology in the Humanities at the University of Maryland, and Research Councils UK. Shared Horizons will create opportunities for disciplinary cross-fertilization through a mix of formal and informal presentations, combined with breakout sessions designed to promote a rich exchange of ideas about how large-scale quantitative methods can lead to new understandings of human culture. Bringing together researchers from the digital humanities and bioinformatics communities, the symposium will explore ways in which these two communities might fruitfully collaborate on projects that bridge the humanities and medicine around the topics of sequence alignment and network analysis, two modes of analysis that intersect with “big data.” All Shared Horizons sessions will be live-streamed with a monitored back channel for the public to post/tweet comments. Recordings of all talks will also be posted to the Shared Horizons website, with the ability to comment pre- and post-event.

Publisher Supplied Author Keywords Now Displayed in PubMed!

PubMed now displays author keywords when supplied by publishers. NLM will not review author keywords for accuracy or add them to non-publisher supplied citations. Author keywords can be searched untagged or using the Other Term [OT] or Text Words [TW] tags. Author Keywords are available on the Abstract, MEDLINE, and XML displays. Author keywords are preceded by a KEYWORDS label and appear below the abstract text on the Abstract display:

Screen capture of Author Keywords on the Abstract Display

Author keywords also appear in the OT field of the MEDLINE display, and users of the XML display will see author keywords in the Keyword element of KeywordList.

PubMed History and Search Bar Updates

A “Download History” link will be added to the PubMed, MeSH and NLM Catalog Advanced page History feature. Using this link will generate History entries in the file “history.csv.” Since Microsoft Excel is typically unable to display or print more than a maximum of 1024 characters in a cell, users with long queries may want to open the CSV file with a text editor to display the complete searches.

The search bar will be updated to list up to the last four databases searched at the top of the pull-down database menu. The alphabetic list with all the databases will also include the recently searched databases. Further details about these changes are available in the 2013 January/February issue of the NLM Technical Bulletin.

NCBI Launches “NCBI Insights” Blog

Screenshot of NCBI InsightsIn January 2013, NCBI released a new blog called NCBI Insights. The National Center for Biotechnology Information (NCBI), a division of the U.S. National Library of Medicine, provides access to scientific and biomedical databases, software tools for analyzing molecular data, and performs research in computational biology. Some NCBI resources include PubMed, GenBank, and BLAST. NCBI Insights was created to provide an insider’s perspective to help you better understand NCBI resources, explore issues of scientific interest that drive NCBI resource development, and demonstrate how you can use NCBI resources to help enhance your research.

The blog has four categories of posts:

  • NCBI Explained – Provides an insider’s perspective on NCBI resources and policies to help you better understand NCBI, and avoid some common misconceptions and misunderstandings.
  • What’s New – Introduces new and updated resources, including specific examples that demonstrate how you can use them to enhance your research.
  • Quick Tips and Tricks – Explains how to perform specific tasks using the NCBI website. Selected topics will be chosen based on questions asked and suggestions provided by users.
  • Science Features – Explores current topics in science and demonstrates how you can find relevant data or resources on the NCBI website for further exploration.

This blog is a complement to existing NCBI education and outreach efforts, such as News and Social Media publicity, Webinar and Workshop training programs, and Help Desk user support. Refer to the NCBI Educational Resources web page for more details on these programs. Be sure to check the NCBI Insights Blog regularly!

Newly Maintained MEDLINE for 2013 MeSH Now Available in PubMed

PubMed/MEDLINE citations, the MeSH database, and the NLM Catalog were updated to reflect 2013 MeSH on December 10, 2013. The MeSH translation tables were also updated. Now that end-of-year activities are complete, MEDLINE/PubMed may be searched using 2013 MeSH vocabulary. For details on the data changes, go to MEDLINE Data Changes — 2013. On December 11, NLM resumed daily (Tuesday-Saturday) MEDLINE updates to PubMed, including the backlog of citations indexed since November 14 with 2013 MeSH.

What’s New for 2013 MeSH for Rare Diseases

MeSH uploaded the disease portion of the Online Mendelian Inheritance in Man (OMIM) database available in the Unified Medical Language System. OMIM is a database that catalogues human diseases with genetic components. Although OMIM disease names are available for searches in PubMed, it is often difficult to index and search for the articles on rare diseases with genetic components due to multiple synonyms used by different scientists that often do not overlap. As was done with NIH Office of Rare Diseases and Research (ORDR) disease terms in 2010, OMIM terms were compared to the existing MeSH descriptors and SCR records. When matches were found, OMIM thesaurus tags were added to the matched MeSH record terms. Where there were no string matches, new disease SCRs were created and mapped to descriptor(s) using the Heading Mapped to (HM) field. MeSH created 3,774 new disease SCRs, and identified and tagged 1,498 existing ORDR SCRs as rare diseases with genetic components during the OMIM load. All OMIM disease names therefore will be available starting with MeSH 2013 for indexers and searchers. The use of the HM field in the disease SCRs will lead to more consistent indexing and retrieval for rare genetic diseases.

There were 2,165 terms in 772 descriptors (MeSH headings) matching OMIM terms and therefore, tagged with the Thesaursus ID (TH)=OMIM (2013). An additional 10,286 terms in 5,453 total SCRs (6,331 terms in 3,774 new SCRs and 3,955 terms in 1,498 existing SCRs) were identified during the load. All newly created SCRs were reviewed and mapped to at least one disease descriptor.

The NLM Technical Bulletin article, What’s New for 2013 MeSH, includes additional information on the OMIM tagging. The NLM Technical Bulletin article, What’s New for 2010 MeSH®, has additional information on the 2010 ORDR term merger into the MeSH vocabulary.

The PubReader View: A New Way to Read Articles in PMC

Full PubReader screen showing first page of an article with the journal banner.In order to keep pace with the continuing advances in web technology, PMC has launched PubReader, an alternative web presentation that offers another, more reader-friendly view of the articles in the PMC archive. Designed particularly for enhancing the readability of PMC journal articles on tablet and other small screen devices, PubReader can also be used on desktops and laptops and from multiple web browsers.

Like a printed paper, PubReader breaks an article into multiple columns and pages to improve readability and navigation. PubReader can expand a page to whatever fits on your screen — with multiple columns on a desktop monitor or a single column page on a small tablet. It will even switch to two columns if you rotate the tablet to a landscape view. When you adjust the font size or change the size of the browser window, page boundaries and columns are adjusted automatically.

PubReader can be activated by selecting the PubReader Format in the right-hand column of individual PMC articles. Additional information can be found in the NLM Technical Bulletin and the PubReader About webpage.

PubMed® for Trainers at UCLA

Do you train others to use PubMed? If so, join us for PubMed for Trainers, a hybrid class with three online sessions and one in-person session. The class is eligible for 15 MLA CE credits. The class is an in-depth look at PubMed and a chance to share training ideas with your fellow participants.

More details about the PubMed for Trainers course and registration in Los Angeles is available! This course is taught by trainers from the  National Library of Medicine Training Center (NTC).

National Library of Medicine ALTBIB Portal Gets Refreshed!

NLM’s ALTBIB portal has been updated. ALTBIB provides access to PubMed/MEDLINE citations relevant to alternatives to the use of live vertebrates in biomedical research and testing. Many of the citations provide access to free full text of the article. The site’s topics and subtopics are aligned with current approaches. For example, information is provided on in silico, in vitro, and improved (refined) animal testing methods. Strategies which incorporate validated methods and other approaches are also covered.

ALTBIB also provides access to animal alternatives news sources, such as the Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM). The portal has an extensive collection of links to key organizations providing information on alternatives to animal testing. ALTBIB provides access to ICCVAM’s “International Acceptance of Alternative Methods, 1998-2012” and “U.S. and International Milestones in Alternative Test Method Development and Evaluations.”

In addition to the topic area PubMed searches, the ALTBIB portal includes a searchable bibliographic collection on alternatives to animal testing. This collection provides citations from published articles, books, book chapters, and technical reports published from 1980 to 2000. The bibliography features citations concerning methods, tests, assays, and procedures that may prove useful in establishing alternatives to the use of intact vertebrates. The ALTBIB bibliographic collection has not been updated since 2001, when the preformulated searches of PubMed were substituted for collecting a formal bibliography.

PubMed for Handhelds App Available!

PubMed for Handhelds (PubMed4Hh) app is now available for free in the iTunes store.

This is an alternative to saving the PubMed for Handhelds web site as a mobile site. Remember to check out the NLM Gallery of Mobile Apps and Sites to see what’s newly listed!